Merge hooks and custom-tools into unified extensions system (#454)

Breaking changes:
- Settings: 'hooks' and 'customTools' arrays replaced with 'extensions'
- CLI: '--hook' and '--tool' flags replaced with '--extension' / '-e'
- API: HookMessage renamed to CustomMessage, role 'hookMessage' to 'custom'
- API: FileSlashCommand renamed to PromptTemplate
- API: discoverSlashCommands() renamed to discoverPromptTemplates()
- Directories: commands/ renamed to prompts/ for prompt templates

Migration:
- Session version bumped to 3 (auto-migrates v2 sessions)
- Old 'hookMessage' role entries converted to 'custom'

Structural changes:
- src/core/hooks/ and src/core/custom-tools/ merged into src/core/extensions/
- src/core/slash-commands.ts renamed to src/core/prompt-templates.ts
- examples/hooks/ and examples/custom-tools/ merged into examples/extensions/
- docs/hooks.md and docs/custom-tools.md merged into docs/extensions.md

New test coverage:
- test/extensions-runner.test.ts (10 tests)
- test/extensions-discovery.test.ts (26 tests)
- test/prompt-templates.test.ts

packages/coding-agent/examples/extensions/with-deps/.gitignore

@@ -0,0 +1 @@
+node_modules/

packages/coding-agent/examples/extensions/with-deps/index.ts

@@ -0,0 +1,40 @@
+/**
+ * Example extension with its own npm dependencies.
+ * Tests that jiti resolves modules from the extension's own node_modules.
+ *
+ * Requires: npm install in this directory
+ */
+
+import type { ExtensionAPI } from "@mariozechner/pi-coding-agent";
+import { Type } from "@sinclair/typebox";
+import ms from "ms";
+
+export default function (pi: ExtensionAPI) {
+	// Use the ms package to prove it loaded
+	const uptime = ms(process.uptime() * 1000, { long: true });
+	console.log(`[with-deps] Extension loaded. Process uptime: ${uptime}`);
+
+	// Register a tool that uses ms
+	pi.registerTool({
+		name: "parse_duration",
+		label: "Parse Duration",
+		description: "Parse a human-readable duration string (e.g., '2 days', '1h', '5m') to milliseconds",
+		parameters: Type.Object({
+			duration: Type.String({ description: "Duration string like '2 days', '1h', '5m'" }),
+		}),
+		execute: async (_toolCallId, params) => {
+			const result = ms(params.duration as ms.StringValue);
+			if (result === undefined) {
+				return {
+					content: [{ type: "text", text: `Invalid duration: "${params.duration}"` }],
+					isError: true,
+					details: {},
+				};
+			}
+			return {
+				content: [{ type: "text", text: `${params.duration} = ${result} milliseconds` }],
+				details: {},
+			};
+		},
+	});
+}

packages/coding-agent/examples/extensions/with-deps/package-lock.json

@@ -0,0 +1,31 @@
+{
+  "name": "pi-extension-with-deps",
+  "version": "1.0.0",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "pi-extension-with-deps",
+      "version": "1.0.0",
+      "dependencies": {
+        "ms": "^2.1.3"
+      },
+      "devDependencies": {
+        "@types/ms": "^2.1.0"
+      }
+    },
+    "node_modules/@types/ms": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/@types/ms/-/ms-2.1.0.tgz",
+      "integrity": "sha512-GsCCIZDE/p3i96vtEqx+7dBUGXrc7zeSK3wwPHIaRThS+9OhWIXRqzs4d6k1SVU8g91DrNRWxWUGhp5KXQb2VA==",
+      "dev": true,
+      "license": "MIT"
+    },
+    "node_modules/ms": {
+      "version": "2.1.3",
+      "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
+      "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==",
+      "license": "MIT"
+    }
+  }
+}

packages/coding-agent/examples/extensions/with-deps/package.json

@@ -0,0 +1,16 @@
+{
+  "name": "pi-extension-with-deps",
+  "version": "1.0.0",
+  "type": "module",
+  "pi": {
+    "extensions": [
+      "./index.ts"
+    ]
+  },
+  "dependencies": {
+    "ms": "^2.1.3"
+  },
+  "devDependencies": {
+    "@types/ms": "^2.1.0"
+  }
+}